Re: [AMBER] Segmentation fault in tleap

From: case <>
Date: Fri, 11 Oct 2013 20:57:04 -0400

On Fri, Oct 11, 2013, wrote:
> PFB1.pdb was created through JSME editor and converted from smiles format,
> and ran through antechamber.
> ATOM 1 F 0 2.065 -0.898 1.142 0.00 0.00 F+0

The "problem" is above: the residue name is blank. Antechamber uses that to
construct a MOL2 file, but the MOL2 format doesn't really allow blanks there.

I don't think PDB files with blank residue names are really "legal", but
antechamber should check for that, and insert a placeholder. For now, you
should construct PDB-format files that have something other than blanks in the
residue columns (18-20).


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Received on Fri Oct 11 2013 - 18:00:02 PDT
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